Small-angle neutron scattering has been used to study the vortex lattice in superconducting MgB2 doped with either manganese or carbon to achieve a similar suppression of the critical temperature. Measurements were performed with the magnetic field applied along the c axis, where the vortex lattice in pure MgB2 is known to undergo a field- and temperature-driven 30° rotation transition. For Mn doping, the vortex lattice phase diagram remains qualitatively similar to that of pure MgB2, indicating only a modest effect on the vortex–vortex interaction. In contrast, the vortex lattice rotation transition is completely suppressed in the C-doped case, probably due to a change in the electronic structure which affects the two-band/two-gap nature of superconductivity in MgB2. The vortex lattice longitudinal correlation length shows the opposite behavior, remaining roughly unchanged between pure and C-doped MgB2 while it is significantly reduced in the Mn-doped case. However, the extensive vortex lattice metastability and related activated behavior, observed in conjunction with the vortex lattice transition in pure MgB2, are also seen in the Mn-doped sample. This shows that the vortex lattice disordering is not associated with a substantially increased vortex pinning.